protein-folding

There are 9 repositories under protein-folding topic.

lucidrains / alphafold2
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
artificial-intelligence attention-mechanism deep-learning protein-folding
Language:Python 1500
PaddlePaddle / PaddleHelix
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
biocomputing ddi deeplearning dti graph-networks machine-learning molecule-design ppi protein-design protein-docking protein-folding protein-structure-prediction representation-learning rna-structure-prediction self-supervised-learning
Language:Python 786
FastFold
hpcaitech / FastFold
Optimizing AlphaFold Training and Inference on GPU Clusters
alphafold2 protein-structure pytorch gpu evoformer parallelism protein-folding cuda habana-gaudi
Language:Python 541
RosettaCommons / PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
dna google-colab jupyter-notebook protein-design protein-docking protein-folding protein-structure-prediction pyrosetta rna-structure-prediction rosetta
Language:Jupyter Notebook 422
lucidrains / equiformer-pytorch
Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding
artificial-intelligence deep-learning equivariance transformers attention-mechanisms protein-folding molecules
Language:Python 225
lucidrains / invariant-point-attention
Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorch module
artificial-intelligence deep-learning protein-folding
Language:Python 137
lucidrains / tr-rosetta-pytorch
Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design
artificial-intelligence deep-learning protein-design protein-folding
Language:Python 78
instadeepai / manyfold
🧬 ManyFold: An efficient and flexible library for training and validating protein folding models
bioinformatics deep-learning jax protein-folding protein-structure python research
Language:Python 72
FrameDiPT
instadeepai / FrameDiPT
FrameDiPT: an SE(3) diffusion model for protein structure inpainting
alphafold2 diffusion-models generative-model inpainting loop-design protein-folding protein-structure tcr
Language:Jupyter Notebook 41
nf-core / proteinfold
Protein 3D structure prediction pipeline
workflow protein-structure protein-sequences protein-folding protein-fold-prediction alphafold2 pipeline nextflow nf-core
Language:Nextflow 40
torchmd / torchmd-cg
Example to fit parameters and run CG simulations using TorchMD and Schnet
coarse-grained-molecular-dynamics protein-folding pytorch machine-learning
Language:Jupyter Notebook 39
lucidrains / triangle-multiplicative-module
Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or columns of a 2d feature map, as a standalone package for Pytorch
artificial-intelligence deep-learning protein-folding
Language:Python 29
prehensilecode / alphafold_singularity
Singularity recipe for AlphaFold
alphafold apptainer containerization containers high-performance-computing hpc protein-folding singularity slurm
Language:Python 27
Bhattacharya-Lab / PolyFold
An interactive visual simulator for distance-based protein folding
protein-folding protein-dynamics stochastic-optimization protein-structure-prediction
Language:Java 24
aws-samples / aws-rosettafold
Infrastructure template and Jupyter notebooks for running RoseTTAFold on AWS Batch.
rosettafold alphafold2 deep-learning aws aws-batch protein-folding hpc
Language:Python 22
thuxugang / opus_fold
OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling
opus-fold protein-contact-map protein-folding protein-potential-functions protein-scoring-functions protein-secondary-structure protein-side-chain-modeling protein-strucutre-prediction protein-torsion-angles
20
MasterMSM
BioKT / MasterMSM
Python package for generating Markov state models
markov-state-model molecular-dynamics protein-folding
Language:Python 18
OkkeVanEck / prospr
Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.
protein structure-prediction protein-folding toolbox cpp python package protein-structure-prediction datasets high-performance-computing computational-science bioinformatics
Language:C++ 18
conradry / prtm
Deep learning for protein science
deep-learning drug-discovery protein-design protein-folding protein-science
Language:Python 16
sarisabban / RosettaAbinitio
A bash script for an automated Rosetta Abinitio folding simulation on an HPC
ab-initio hpc rosetta rosetta-abinitio protein-folding proteins job-scheduler pbs sari plotting score
Language:Shell 11
johnnytam100 / awesome-protein-design
A curated list of awesome protein design research, software and resources.
alphafold alphafold-multimer alphafold2 bioinformatics bioinformatics-tool molecular-biology protein-design protein-function protein-sequence protein-structure structural-bioinformatics structural-biology protein-engineering protein-folding protein-protein-interaction protein-structure-prediction
10
PhilippThoelke / protein-folding
Protein structure prediction using optimization methods from the field of machine learning
protein-folding protein-structure-prediction gradient-descent minimization
Language:Jupyter Notebook 10
AMarinhoSN / FleXgeo
A package for protein conformational ensemble analyses based on a differential geometry representation of protein backbones.
protein-backbones analyses protein-dynamics protein-folding differential-geometry
Language:Python 8
ps4-dataset
omarperacha / ps4-dataset
The largest open-source dataset for Protein Single Sequence Secondary Structure prediction.
bioinformatics database deep-learning machine-learning protein-folding protein-structure
Language:Python 7
lorenzoditucci / sda_examples_aws
Examples for SDAccel 2017.1+ on AWS F1 instances
sdaccel aws aws-f1 smith-waterman protein-folding examples
Language:C++ 6
moldyn / HP35
Selecting Features for Markov Modeling: A Case Study on HP35
benchmark-system hp35 markov-model protein-folding
Language:HiveQL 6
renatawong / quantum-protein-structure-prediction
Quantum algorithms for protein structure prediction. Language: Python (Qiskit). Platform: IBM Quantum's backends and simulators.
quantum-algorithms protein-structure-prediction qiskit protein-folding protein-structure quantum-computing
Language:Jupyter Notebook 6
vvoelz / HPSandbox
a package of Python modules and example scripts for experimenting with the two-dimensional HP lattice model of Dill and Chan.
biophysics protein-folding statistical-mechanics python
Language:Python 5
JosephPB / Protein
Protein folding simulator
biology protein protein-folding
Language:C++ 4
berylgithub / HP-Protein
numerical-optimization protein-folding computational-biology
Language:Jupyter Notebook 3
lellew / Peptide_Folding_Classifier
We seek a classifier that will predict if a protein sequence (+3D coordinates) will fold.
deep-learning machine-learning protein-fold-prediction protein-folding
Language:Python 3
alvinwatner / HP_Protein_Fold-GymEnv
"Train Your Reinforcement Learning Algorithm To This Protein Folding Problem Simulation". This is part of my bachelor thesis. The latest version of this env is in the LogDQN_ProteinHP repository.
reinforcement-learning simulation python protein-folding
Language:Python 2
AndersJing / ResNetQA
ResNetQA: Improved protein model quality assessment by integrating sequential and pairwise features using deep learning
protein-folding protein-model-quality-assessment protein-model-quality-estimation protein-structure-prediction
Language:Python 2
Bhattacharya-Lab / DConStruct
Hybridized distance- and contact-based hierarchical protein folding
protein-folding protein-modeling abinitio-simulations protein-structure-prediction
Language:Python 2
jhrcook / proof-of-concept-alphafold
A proof-of-concept for using AlphaFold with new amino acid sequences (this may change to a full project in the future).
alphafold python3 tensorflow jupyterlab bioinformatics protein-folding
Language:Shell 2
thuxugang / opus_fold3
OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow
cryo-em gradient-based-folding protein-docking protein-folding protein-structure
Language:Python 2

protein-folding

lucidrains / alphafold2

PaddlePaddle / PaddleHelix

hpcaitech / FastFold

RosettaCommons / PyRosetta.notebooks

lucidrains / equiformer-pytorch

lucidrains / invariant-point-attention

lucidrains / tr-rosetta-pytorch

instadeepai / manyfold

instadeepai / FrameDiPT

nf-core / proteinfold

torchmd / torchmd-cg

lucidrains / triangle-multiplicative-module

prehensilecode / alphafold_singularity

Bhattacharya-Lab / PolyFold

aws-samples / aws-rosettafold

thuxugang / opus_fold

BioKT / MasterMSM

OkkeVanEck / prospr

conradry / prtm

sarisabban / RosettaAbinitio

johnnytam100 / awesome-protein-design

PhilippThoelke / protein-folding

AMarinhoSN / FleXgeo

omarperacha / ps4-dataset

lorenzoditucci / sda_examples_aws

moldyn / HP35

renatawong / quantum-protein-structure-prediction

vvoelz / HPSandbox

JosephPB / Protein

berylgithub / HP-Protein

lellew / Peptide_Folding_Classifier

alvinwatner / HP_Protein_Fold-GymEnv

AndersJing / ResNetQA

Bhattacharya-Lab / DConStruct

jhrcook / proof-of-concept-alphafold

thuxugang / opus_fold3